Metabolicaly-driven interactions between biological species in any local ecosystem typically form large, complex networks that generate interesting and often unpredictable system dynamics. A new Mount Everest for theoretical biology, with a wide range of applications, is the development of methods to control and engineer these complex, nonlinear systems. To this end, we need to understand a fundamental problem that has occupied Biologists, and in particular, Ecologists, for almost two centuries: how do these seemingly improbable systems assemble and persist in (an increasingly) fluctuating and uncertain real world? In this talk, I will outline the challenge, and present recent progress towards the goal of engineering microbiomes under a ubiquitous source of environmental fluctuations: temperature.